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Yorodumi- PDB-3fbk: Crystal structure of the C2 domain of the human regulator of G-pr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fbk | ||||||
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Title | Crystal structure of the C2 domain of the human regulator of G-protein signaling 3 isoform 6 (RGP3), Northeast Structural Genomics Consortium Target HR5550A | ||||||
Components | Regulator of G-protein signaling 3 | ||||||
Keywords | SIGNALING PROTEIN / all beta-sheet fold / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Alternative splicing / Cell membrane / Cytoplasm / Membrane / Nucleus / Phosphoprotein / Signal transduction inhibitor | ||||||
Function / homology | Function and homology information regulation of G protein-coupled receptor signaling pathway / negative regulation of signal transduction / GTPase activator activity / G alpha (i) signalling events / G alpha (q) signalling events / G protein-coupled receptor signaling pathway / GTPase activity / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Forouhar, F. / Lew, S. / Seetharaman, J. / Mao, L. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Shastry, R. / Everett, J.K. / Nair, R. ...Forouhar, F. / Lew, S. / Seetharaman, J. / Mao, L. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Shastry, R. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the C2 domain of the human regulator of G-protein signaling 3 isoform 6 (RGP3), Northeast Structural Genomics Consortium Target HR5550A Authors: Forouhar, F. / Lew, S. / Seetharaman, J. / Mao, L. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Shastry, R. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fbk.cif.gz | 72.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fbk.ent.gz | 52.9 KB | Display | PDB format |
PDBx/mmJSON format | 3fbk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fb/3fbk ftp://data.pdbj.org/pub/pdb/validation_reports/fb/3fbk | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17709.023 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RGS3 / Plasmid: pET14-15C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: P49796 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.54 % |
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Crystal grow | Temperature: 291 K / Method: microbatch under oil / pH: 7 Details: Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT. Reservoir solution: 100 mM Bis-Tris Propane (pH 7), 40% PEG 1000, and 100 mM (NH4)2 SO4. , microbatch under oil, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97905 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 13, 2008 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97905 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 36846 / Num. obs: 35631 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 6.6 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.058 / Net I/σ(I): 16.16 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 4.91 / Num. unique all: 3712 / Rsym value: 0.15 / % possible all: 94.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→19.58 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 650860.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.9417 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→19.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 10
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